Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011450.1 Kokia drynarioides strain JFW-HI SEQ_126434, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 139678
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 262 characters in sequence are not A, C, G, or T
Found at i:8013 original size:23 final size:23
Alignment explanation
Indices: 7983--8040 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
7973 AGGAACGCTA
7983 GTGTGCTTACTGTTTCGCACTTC
1 GTGTGCTTACTGTTTCGCACTTC
8006 GTGTGCTTACTGTTTCGCACTTC
1 GTGTGCTTACTGTTTCGCACTTC
* *
8029 ATGTGCCTACTG
1 GTGTGCTTACTG
8041 ATTTTCGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.41
Consensus pattern (23 bp):
GTGTGCTTACTGTTTCGCACTTC
Found at i:10079 original size:31 final size:30
Alignment explanation
Indices: 10043--10156 Score: 106
Period size: 31 Copynumber: 3.7 Consensus size: 30
10033 CAACATATGG
10043 AATGTTAGGGCTCACATGAAGGCAACCAATT
1 AATGTTAGGGCTCACAT-AAGGCAACCAATT
* * * * *
10074 AATGTTAGGGTTCGAC-TATGGCAATCTATGG
1 AATGTTAGGGCTC-ACATAAGGCAACCAAT-T
*
10105 AATGTTAGGGCTCACCTGAAGGCAACCAATT
1 AATGTTAGGGCTCACAT-AAGGCAACCAATT
* *
10136 AAT-TCAGGGTTCACATAAGGC
1 AATGTTAGGGCTCACATAAGGC
10157 TGAAGTAATA
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
29 5 0.08
30 21 0.32
31 29 0.44
32 11 0.17
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (30 bp):
AATGTTAGGGCTCACATAAGGCAACCAATT
Found at i:10125 original size:62 final size:61
Alignment explanation
Indices: 10024--10147 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 61
10014 ACTGAGAAAA
*
10024 CGACTATGGCAACATATGGAATGTTAGGGCTCACATGAAGGCAACCAATTAATGTTAGGGTT
1 CGACTATGGCAACATATGGAATGTTAGGGCTCACATGAAGGCAACCAATTAAT-TCAGGGTT
*
10086 CGACTATGGCAATC-TATGGAATGTTAGGGCTCACCTGAAGGCAACCAATTAATTCAGGGTT
1 CGACTATGGCAA-CATATGGAATGTTAGGGCTCACATGAAGGCAACCAATTAATTCAGGGTT
10147 C
1 C
10148 ACATAAGGCT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
61 8 0.14
62 50 0.85
63 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (61 bp):
CGACTATGGCAACATATGGAATGTTAGGGCTCACATGAAGGCAACCAATTAATTCAGGGTT
Found at i:18888 original size:18 final size:18
Alignment explanation
Indices: 18865--18900 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18855 ATTCAATCCC
18865 TTTAAAATTTTTTTAATA
1 TTTAAAATTTTTTTAATA
*
18883 TTTAAATTTTTTTTAATA
1 TTTAAAATTTTTTTAATA
18901 CAATGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAAAATTTTTTTAATA
Found at i:23269 original size:23 final size:23
Alignment explanation
Indices: 23242--23291 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
23232 GAACGCTAGC
23242 GTGCTTACTATTTCGCACTTCGT
1 GTGCTTACTATTTCGCACTTCGT
*
23265 GTGCTTACTGTTTCGCACTTCGT
1 GTGCTTACTATTTCGCACTTCGT
23288 GTGC
1 GTGC
23292 CTATTGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.42
Consensus pattern (23 bp):
GTGCTTACTATTTCGCACTTCGT
Found at i:23333 original size:22 final size:23
Alignment explanation
Indices: 23290--23342 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
23280 CACTTCGTGT
* *
23290 GCCTATTGATTTGCGCTATGTGC
1 GCCTACTGATTTGCACTATGTGC
* *
23313 GCCTACTGA-TTGCACTGTGTGT
1 GCCTACTGATTTGCACTATGTGC
*
23335 GCTTACTG
1 GCCTACTG
23343 TTAAGTACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (23 bp):
GCCTACTGATTTGCACTATGTGC
Found at i:30642 original size:29 final size:29
Alignment explanation
Indices: 30583--30641 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
30573 TTTAGTTTAA
* *
30583 TGTGCAATTTTTTACATGAACTTTGATTT
1 TGTGCAATTTTATACATAAACTTTGATTT
*
30612 TGTGCAATTTTATACATAAAATTTTGATTT
1 TGTGCAATTTTATACAT-AAACTTTGATTT
30642 GATCCAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (29 bp):
TGTGCAATTTTATACATAAACTTTGATTT
Found at i:50893 original size:6 final size:6
Alignment explanation
Indices: 50879--50909 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
50869 AAACAGCACG
*
50879 AACAGC AACATC AACATC AACATC AACATC A
1 AACATC AACATC AACATC AACATC AACATC A
50910 TGTCCATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.52, C:0.32, G:0.03, T:0.13
Consensus pattern (6 bp):
AACATC
Found at i:51401 original size:7 final size:7
Alignment explanation
Indices: 51378--51410 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
51368 AAAACAAATA
51378 CAAAAG-
1 CAAAAGT
51384 CAAAGAGT
1 CAAA-AGT
51392 CAAAAGT
1 CAAAAGT
51399 CAAAAGT
1 CAAAAGT
51406 CAAAA
1 CAAAA
51411 TCACTGGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.16
7 17 0.68
8 4 0.16
ACGTcount: A:0.61, C:0.15, G:0.15, T:0.09
Consensus pattern (7 bp):
CAAAAGT
Found at i:55704 original size:30 final size:30
Alignment explanation
Indices: 55670--55737 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
55660 ATTTTAAAGT
55670 ATTTTTCATAAATATTTTTAAAAAATATTA
1 ATTTTTCATAAATATTTTTAAAAAATATTA
55700 ATTTTTCATAAATATTTTTAAAAAATATTA
1 ATTTTTCATAAATATTTTTAAAAAATATTA
*
55730 AATTTTCA
1 ATTTTTCA
55738 AGAATCTACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTTTCATAAATATTTTTAAAAAATATTA
Found at i:55705 original size:17 final size:17
Alignment explanation
Indices: 55683--55735 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 17
55673 TTTCATAAAT
55683 ATTTTTAAAAAATATTA
1 ATTTTTAAAAAATATTA
* *
55700 ATTTTT-CATAA-A-T-
1 ATTTTTAAAAAATATTA
55713 ATTTTTAAAAAATATTAA
1 ATTTTTAAAAAATATT-A
55731 ATTTT
1 ATTTT
55736 CAAGAATCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 2 0.07
16 4 0.15
17 6 0.22
18 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTTAAAAAATATTA
Found at i:57340 original size:18 final size:18
Alignment explanation
Indices: 57317--57359 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
57307 GTTTAAGGTC
57317 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
57335 TAATTAATTAAAATTATT
1 TAATTAATTAAAATTATT
57353 TAATTAA
1 TAATTAA
57360 AAATCTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:57505 original size:15 final size:15
Alignment explanation
Indices: 57485--57535 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
57475 ATAAAACGAT
57485 AATATAAATAATTAA
1 AATATAAATAATTAA
* *
57500 AATAT-AATATTTTA
1 AATATAAATAATTAA
*
57514 AATATAAATTATTAA
1 AATATAAATAATTAA
57529 AATATAA
1 AATATAA
57536 TCTAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:57516 original size:14 final size:14
Alignment explanation
Indices: 57485--57536 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
57475 ATAAAACGAT
* *
57485 AATATAAATAATTAA
1 AATAT-AATATTTTA
57500 AATATAATATTTTA
1 AATATAATATTTTA
57514 AATATAA-ATTATTAA
1 AATATAATATT-TT-A
57529 AATATAAT
1 AATATAAT
57537 CTAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 3 0.09
14 16 0.50
15 13 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATATTTTA
Found at i:57549 original size:29 final size:29
Alignment explanation
Indices: 57488--57550 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
57478 AAACGATAAT
*** *
57488 ATAAATAATTAAAATATAATATTTTAAAT
1 ATAAATAATTAAAATATAATATAAAAAAA
* *
57517 ATAAATTATTAAAATATAATCTAAAAAAA
1 ATAAATAATTAAAATATAATATAAAAAAA
57546 ATAAA
1 ATAAA
57551 AGTGATTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
ATAAATAATTAAAATATAATATAAAAAAA
Found at i:78637 original size:23 final size:23
Alignment explanation
Indices: 78603--78654 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
78593 GACCTTAGCT
*
78603 TTTGATCTACAGTTACAAGTCAA
1 TTTGATCCACAGTTACAAGTCAA
78626 TTTGATCCACAGTTACAAGTCAA
1 TTTGATCCACAGTTACAAGTCAA
78649 TTTGAT
1 TTTGAT
78655 ACAAGAACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (23 bp):
TTTGATCCACAGTTACAAGTCAA
Found at i:80837 original size:26 final size:26
Alignment explanation
Indices: 80808--80859 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
80798 AAATAAATAG
*
80808 TTAATAGAATCAGTTGATCAAATTAA
1 TTAATAGAATCAATTGATCAAATTAA
*
80834 TTAATAGAATCAATTGGTCAAATTAA
1 TTAATAGAATCAATTGATCAAATTAA
80860 ATTATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (26 bp):
TTAATAGAATCAATTGATCAAATTAA
Found at i:81591 original size:15 final size:16
Alignment explanation
Indices: 81571--81600 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
81561 CACCTCTATT
81571 TAAAAG-ACAATATAG
1 TAAAAGTACAATATAG
81586 TAAAAGTACAATATA
1 TAAAAGTACAATATA
81601 TTAGAATGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (16 bp):
TAAAAGTACAATATAG
Found at i:95908 original size:17 final size:17
Alignment explanation
Indices: 95880--95918 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
95870 TTGAATTAAT
95880 TTTTTTATTTTTAATATA
1 TTTTTTATTTTTAATA-A
95898 TTTTTTATTTTT-ATAA
1 TTTTTTATTTTTAATAA
95914 TTTTT
1 TTTTT
95919 AAATAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.29
17 3 0.14
18 12 0.57
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTATTTTTAATAA
Found at i:122706 original size:18 final size:18
Alignment explanation
Indices: 122683--122725 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
122673 AATCAGTGAT
122683 ATATATATATACACATAC
1 ATATATATATACACATAC
* ***
122701 ATATATGTATATGTATAC
1 ATATATATATACACATAC
122719 ATATATA
1 ATATATA
122726 ATGTTGCAGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (18 bp):
ATATATATATACACATAC
Found at i:123113 original size:3 final size:3
Alignment explanation
Indices: 123105--123133 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
123095 GCACCAGTAT
123105 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
123134 CATGGATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:124997 original size:21 final size:21
Alignment explanation
Indices: 124971--125011 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
124961 ATGGCAGTTA
124971 GATTTACAT-TATTAAAAATTT
1 GATTTA-ATCTATTAAAAATTT
*
124992 GATTTAATCTTTTAAAAATT
1 GATTTAATCTATTAAAAATT
125012 ATAAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (21 bp):
GATTTAATCTATTAAAAATTT
Found at i:133055 original size:46 final size:46
Alignment explanation
Indices: 132996--133083 Score: 176
Period size: 46 Copynumber: 1.9 Consensus size: 46
132986 CAAGTCCACC
132996 TATTGATCGTGCTTGACAACAATCATCCCATTTAACTAAAGTCGAT
1 TATTGATCGTGCTTGACAACAATCATCCCATTTAACTAAAGTCGAT
133042 TATTGATCGTGCTTGACAACAATCATCCCATTTAACTAAAGT
1 TATTGATCGTGCTTGACAACAATCATCCCATTTAACTAAAGT
133084 TGGTTTATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (46 bp):
TATTGATCGTGCTTGACAACAATCATCCCATTTAACTAAAGTCGAT
Done.